biotite 1.3.0__cp311-cp311-win_amd64.whl → 1.4.0__cp311-cp311-win_amd64.whl

biotite/interface/pymol/object.py

@@ -388,7 +388,9 @@ class PyMOLObject:
         elif isinstance(selection, str):
             return f"%{self._name} and ({selection})"
         else:
-            sel = self.where(np.asarray(selection))
+            if not isinstance(selection, slice):
+                selection = np.asarray(selection)
+            sel = self.where(selection)
             if sel == "none" and not_none:
                 raise ValueError("Selection contains no atoms")
             return sel

biotite/interface/rdkit/mol.py

@@ -59,7 +59,7 @@ _STANDARD_ANNOTATIONS = frozenset(
         "charge",
         "b_factor",
         "occupancy",
-        "label_alt_id",
+        "altloc_id",
     }
 )
 
@@ -202,8 +202,8 @@ def to_mol(
             rdkit_atom_res_info.SetOccupancy(atoms.occupancy[i].item())
         if "b_factor" in has_annot:
             rdkit_atom_res_info.SetTempFactor(atoms.b_factor[i].item())
-        if "label_alt_id" in has_annot:
-            rdkit_atom_res_info.SetAltLoc(atoms.label_alt_id[i].item())
+        if "altloc_id" in has_annot:
+            rdkit_atom_res_info.SetAltLoc(atoms.altloc_id[i].item())
         rdkit_atom.SetPDBResidueInfo(rdkit_atom_res_info)
 
         # add extra annotations
@@ -361,7 +361,7 @@ def from_mol(mol, conformer_id=None, add_hydrogen=None):
     atoms.add_annotation("charge", int)
     atoms.add_annotation("b_factor", float)
     atoms.add_annotation("occupancy", float)
-    atoms.add_annotation("label_alt_id", str)
+    atoms.add_annotation("altloc_id", str)
 
     for rdkit_atom in rdkit_atoms:
         _atom_idx = rdkit_atom.GetIdx()
@@ -406,7 +406,7 @@ def from_mol(mol, conformer_id=None, add_hydrogen=None):
         atoms.res_id[_atom_idx] = residue_info.GetResidueNumber()
         atoms.ins_code[_atom_idx] = residue_info.GetInsertionCode()
         atoms.res_name[_atom_idx] = residue_info.GetResidueName()
-        atoms.label_alt_id[_atom_idx] = residue_info.GetAltLoc()
+        atoms.altloc_id[_atom_idx] = residue_info.GetAltLoc()
         atoms.hetero[_atom_idx] = residue_info.GetIsHeteroAtom()
         atoms.b_factor[_atom_idx] = residue_info.GetTempFactor()
         atoms.occupancy[_atom_idx] = residue_info.GetOccupancy()

biotite/structure/bonds.pyx

@@ -517,14 +517,41 @@ class BondList(Copyable):
         0 1 SINGLE
         1 2 DOUBLE
         """
-        bond_types = self._bonds[:,2]
         for aromatic_type, non_aromatic_type in [
             (BondType.AROMATIC_SINGLE, BondType.SINGLE),
             (BondType.AROMATIC_DOUBLE, BondType.DOUBLE),
             (BondType.AROMATIC_TRIPLE, BondType.TRIPLE),
             (BondType.AROMATIC, BondType.ANY),
         ]:
-            bond_types[bond_types == aromatic_type] = non_aromatic_type
+            mask = self._bonds[:, 2] == aromatic_type
+            self._bonds[mask, 2] = non_aromatic_type
+
+    def remove_kekulization(self):
+        """
+        Remove the bond order information from aromatic bonds, i.e. convert all
+        aromatic bonds to :attr:`BondType.ANY`.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(3)
+        >>> bond_list.add_bond(0, 1, BondType.AROMATIC_SINGLE)
+        >>> bond_list.add_bond(1, 2, BondType.AROMATIC_DOUBLE)
+        >>> bond_list.remove_kekulization()
+        >>> for i, j, bond_type in bond_list.as_array():
+        ...     print(i, j, BondType(bond_type).name)
+        0 1 AROMATIC
+        1 2 AROMATIC
+        """
+        kekulized_mask = np.isin(
+            self._bonds[:, 2],
+            (
+                BondType.AROMATIC_SINGLE,
+                BondType.AROMATIC_DOUBLE,
+                BondType.AROMATIC_TRIPLE,
+            ),
+        )
+        self._bonds[kekulized_mask, 2] = BondType.AROMATIC
 
     def remove_bond_order(self):
         """
@@ -532,6 +559,41 @@ class BondList(Copyable):
         """
         self._bonds[:,2] = BondType.ANY
 
+    def convert_bond_type(self, original_bond_type, new_bond_type):
+        """
+        convert_bond_type(original_bond_type, new_bond_type)
+
+        Convert all occurences of a given bond type into another bond type.
+
+        Parameters
+        ----------
+        original_bond_type : BondType or int
+            The bond type to convert.
+        new_bond_type : BondType or int
+            The new bond type.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(4)
+        >>> bond_list.add_bond(0, 1, BondType.DOUBLE)
+        >>> bond_list.add_bond(1, 2, BondType.COORDINATION)
+        >>> bond_list.add_bond(2, 3, BondType.COORDINATION)
+        >>> for i, j, bond_type in bond_list.as_array():
+        ...     print(i, j, BondType(bond_type).name)
+        0 1 DOUBLE
+        1 2 COORDINATION
+        2 3 COORDINATION
+        >>> bond_list.convert_bond_type(BondType.COORDINATION, BondType.SINGLE)
+        >>> for i, j, bond_type in bond_list.as_array():
+        ...     print(i, j, BondType(bond_type).name)
+        0 1 DOUBLE
+        1 2 SINGLE
+        2 3 SINGLE
+        """
+        mask = self._bonds[:, 2] == original_bond_type
+        self._bonds[mask, 2] = new_bond_type
+
     def get_atom_count(self):
         """
         get_atom_count()
@@ -1437,9 +1499,8 @@ _DEFAULT_DISTANCE_RANGE = {
 def connect_via_distances(atoms, dict distance_range=None, bint inter_residue=True,
                           default_bond_type=BondType.ANY, bint periodic=False):
     """
-    connect_via_distances(atoms, distance_range=None, atom_mask=None,
-                          inter_residue=True, default_bond_type=BondType.ANY,
-                          periodic=False)
+    connect_via_distances(atoms, distance_range=None, inter_residue=True,
+                          default_bond_type=BondType.ANY, periodic=False)
 
     Create a :class:`BondList` for a given atom array, based on
     pairwise atom distances.
@@ -1589,7 +1650,7 @@ def connect_via_distances(atoms, dict distance_range=None, bint inter_residue=Tr
 def connect_via_residue_names(atoms, bint inter_residue=True,
                               dict custom_bond_dict=None):
     """
-    connect_via_residue_names(atoms, atom_mask=None, inter_residue=True)
+    connect_via_residue_names(atoms, inter_residue=True, custom_bond_dict=None)
 
     Create a :class:`BondList` for a given atom array (stack), based on
     the deposited bonds for each residue in the RCSB ``components.cif``

biotite/structure/box.py

@@ -361,7 +361,7 @@ def repeat_box(atoms, amount=1):
     if atoms.box is None:
         raise BadStructureError("Structure has no box")
 
-    repeat_coord, indices = repeat_box_coord(atoms.coord, atoms.box)
+    repeat_coord, indices = repeat_box_coord(atoms.coord, atoms.box, amount)
     # Unroll repeated coordinates for input to 'repeat()'
     if repeat_coord.ndim == 2:
         repeat_coord = repeat_coord.reshape(-1, atoms.array_length(), 3)

biotite/structure/compare.py

@@ -449,6 +449,8 @@ def lddt(
     # Aggregate the fractions over the desired level
     if isinstance(aggregation, str) and aggregation == "all":
         # Average over all contacts
+        if len(fraction_preserved_bins) == 0:
+            return np.float32(np.nan)
         return np.mean(fraction_preserved_bins, axis=-1)
     else:
         # A string is also a 'Sequence'

biotite/structure/io/pdb/file.py

@@ -936,7 +936,11 @@ class PDBFile(TextFile):
             if transform_start is None:
                 raise InvalidFileError("No 'BIOMT' records found for chosen assembly")
             rotations, translations = _parse_transformations(
-                assembly_lines[transform_start:stop]
+                [
+                    line
+                    for line in assembly_lines[transform_start:stop]
+                    if len(line.strip()) > 0
+                ]
             )
             # Filter affected chains
             sub_structure = structure[
@@ -1193,7 +1197,7 @@ class PDBFile(TextFile):
         conect_lines = [line for line in self.lines if line.startswith("CONECT")]
 
         # Mapping from atom ids to indices in an AtomArray
-        atom_id_to_index = np.zeros(atom_ids[-1] + 1, dtype=int)
+        atom_id_to_index = np.full(atom_ids[-1] + 1, -1, dtype=int)
         try:
             for i, id in enumerate(atom_ids):
                 atom_id_to_index[id] = i
@@ -1202,15 +1206,21 @@ class PDBFile(TextFile):
 
         bonds = []
         for line in conect_lines:
-            center_id = atom_id_to_index[decode_hybrid36(line[6:11])]
+            center_index = atom_id_to_index[decode_hybrid36(line[6:11])]
+            if center_index == -1:
+                # Atom ID is not in the AtomArray (probably removed altloc)
+                continue
             for i in range(11, 31, 5):
                 id_string = line[i : i + 5]
                 try:
-                    id = atom_id_to_index[decode_hybrid36(id_string)]
+                    contact_index = atom_id_to_index[decode_hybrid36(id_string)]
+                    if contact_index == -1:
+                        # Atom ID is not in the AtomArray (probably removed altloc)
+                        continue
                 except ValueError:
                     # String is empty -> no further IDs
                     break
-                bonds.append((center_id, id))
+                bonds.append((center_index, contact_index))
 
         # The length of the 'atom_ids' array
         # is equal to the length of the AtomArray

biotite/structure/io/pdbx/bcif.py

@@ -511,7 +511,7 @@ class BinaryCIFBlock(_HierarchicalContainer):
 
     def __delitem__(self, key):
         try:
-            return super().__setitem__("_" + key)
+            return super().__delitem__("_" + key)
         except KeyError:
             raise KeyError(key)
 
@@ -581,9 +581,12 @@ class BinaryCIFFile(File, _HierarchicalContainer):
 
     @property
     def block(self):
-        if len(self) != 1:
+        if len(self) == 0:
+            raise ValueError("There are no blocks in the file")
+        elif len(self) > 1:
             raise ValueError("There are multiple blocks in the file")
-        return self[next(iter(self))]
+        else:
+            return self[next(iter(self))]
 
     @staticmethod
     def subcomponent_class():

biotite/structure/io/pdbx/cif.py

@@ -799,9 +799,12 @@ class CIFFile(_Component, File, MutableMapping):
 
     @property
     def block(self):
-        if len(self) != 1:
+        if len(self) == 0:
+            raise ValueError("There are no blocks in the file")
+        elif len(self) > 1:
             raise ValueError("There are multiple blocks in the file")
-        return self[next(iter(self))]
+        else:
+            return self[next(iter(self))]
 
     @staticmethod
     def subcomponent_class():

biotite/structure/io/pdbx/compress.py

@@ -56,14 +56,14 @@ def compress(data, float_tolerance=None, rtol=1e-6, atol=1e-4):
     >>> pdbx_file.write(uncompressed_file)
     >>> _ = uncompressed_file.seek(0)
     >>> print(f"{len(uncompressed_file.read()) // 1000} KB")
-    927 KB
+    937 KB
     >>> # Write compressed file
     >>> pdbx_file = compress(pdbx_file)
     >>> compressed_file = BytesIO()
     >>> pdbx_file.write(compressed_file)
     >>> _ = compressed_file.seek(0)
     >>> print(f"{len(compressed_file.read()) // 1000} KB")
-    111 KB
+    114 KB
     """
     if float_tolerance is not None:
         warnings.warn(

biotite/structure/io/pdbx/convert.py

@@ -775,7 +775,10 @@ def _filter_altloc(array, atom_site, altloc):
     if altloc == "all":
         array.set_annotation("altloc_id", altloc_ids.as_array(str))
         return array, atom_site
-    elif altloc_ids is None or (altloc_ids.mask.array != MaskValue.PRESENT).all():
+    elif altloc_ids is None or (
+        altloc_ids.mask is not None
+        and (altloc_ids.mask.array != MaskValue.PRESENT).all()
+    ):
         # No altlocs in atom_site category
         return array, atom_site
     elif altloc == "occupancy" and occupancy is not None:
@@ -873,11 +876,7 @@ def set_structure(
         this parameter is ignored.
         If the file is empty, a new data block will be created.
     include_bonds : bool, optional
-        If set to true and `array` has associated ``bonds`` , the
-        intra-residue bonds will be written into the ``chem_comp_bond``
-        category.
-        Inter-residue bonds will be written into the ``struct_conn``
-        independent of this parameter.
+        DEPRECATED: Has no effect anymore.
     extra_fields : list of str, optional
         List of additional fields from the ``atom_site`` category
         that should be written into the file.
@@ -898,6 +897,13 @@ def set_structure(
     >>> set_structure(file, atom_array)
     >>> file.write(os.path.join(path_to_directory, "structure.cif"))
     """
+    if include_bonds:
+        warnings.warn(
+            "`include_bonds` parameter is deprecated, "
+            "intra-residue are always written, if available",
+            DeprecationWarning,
+        )
+
     _check_non_empty(array)
 
     block = _get_or_create_block(pdbx_file, data_block)
@@ -975,10 +981,9 @@ def set_structure(
         struct_conn = _set_inter_residue_bonds(array, atom_site)
         if struct_conn is not None:
             block["struct_conn"] = struct_conn
-        if include_bonds:
-            chem_comp_bond = _set_intra_residue_bonds(array, atom_site)
-            if chem_comp_bond is not None:
-                block["chem_comp_bond"] = chem_comp_bond
+        chem_comp_bond = _set_intra_residue_bonds(array, atom_site)
+        if chem_comp_bond is not None:
+            block["chem_comp_bond"] = chem_comp_bond
 
     # In case of a single model handle each coordinate
     # simply like a flattened array
@@ -1652,11 +1657,11 @@ def get_assembly(
         If set to true, a :class:`BondList` will be created for the
         resulting :class:`AtomArray` containing the bond information
         from the file.
-        Bonds, whose order could not be determined from the
-        *Chemical Component Dictionary*
-        (e.g. especially inter-residue bonds),
-        have :attr:`BondType.ANY`, since the PDB format itself does
-        not support bond orders.
+        Inter-residue bonds, will be read from the ``struct_conn``
+        category.
+        Intra-residue bonds will be read from the ``chem_comp_bond``, if
+        available, otherwise they will be derived from the Chemical
+        Component Dictionary.
 
     Returns
     -------
@@ -1926,11 +1931,11 @@ def get_unit_cell(
         If set to true, a :class:`BondList` will be created for the
         resulting :class:`AtomArray` containing the bond information
         from the file.
-        Bonds, whose order could not be determined from the
-        *Chemical Component Dictionary*
-        (e.g. especially inter-residue bonds),
-        have :attr:`BondType.ANY`, since the PDB format itself does
-        not support bond orders.
+        Inter-residue bonds, will be read from the ``struct_conn``
+        category.
+        Intra-residue bonds will be read from the ``chem_comp_bond``, if
+        available, otherwise they will be derived from the Chemical
+        Component Dictionary.
 
     Returns
     -------

biotite/structure/rings.py

@@ -8,7 +8,12 @@ This module provides functions related to aromatic rings.
 
 __name__ = "biotite.structure"
 __author__ = "Patrick Kunzmann"
-__all__ = ["find_aromatic_rings", "find_stacking_interactions", "PiStacking"]
+__all__ = [
+    "find_aromatic_rings",
+    "find_stacking_interactions",
+    "find_pi_cation_interactions",
+    "PiStacking",
+]
 
 
 from enum import IntEnum
@@ -268,6 +273,117 @@ def find_stacking_interactions(
     ]
 
 
+def find_pi_cation_interactions(
+    atoms,
+    distance_cutoff=5.0,
+    angle_tol=np.deg2rad(30.0),
+):
+    """
+    Find pi-cation interactions between aromatic rings and cations.
+
+    Parameters
+    ----------
+    atoms : AtomArray
+        The atoms to be searched for pi-cation interactions.
+        Requires an associated :class:`BondList` and ``charge`` annotation.
+    distance_cutoff : float, optional
+        The cutoff distance between ring centroid and cation.
+    angle_tol : float, optional
+        The tolerance for the angle between the ring plane normal
+        and the centroid-cation vector. Perfect pi-cation interaction
+        has 0° angle (perpendicular to ring plane).
+        Given in radians.
+
+    Returns
+    -------
+    interactions : list of tuple(ndarray, int)
+        The pi-cation interactions between aromatic rings and cations.
+        Each element in the list represents one pi-cation interaction.
+        The first element of each tuple represents atom indices of the
+        aromatic ring, the second element is the atom index of the cation.
+
+    See Also
+    --------
+    find_aromatic_rings : Used for finding the aromatic rings in this function.
+    find_stacking_interactions : Find pi-stacking interactions between rings.
+
+    Notes
+    -----
+    The conditions for pi-cation interactions are:
+        - The distance between ring centroid and cation must be within
+          `distance_cutoff`. :footcite:`Wojcikowski2015` uses 5.0 Å,
+          whereas :footcite:`Bouysset2021` uses 4.5 Å.
+        - The angle between the ring plane normal and the centroid-cation
+          vector must be within `angle_tol` of 0° (perpendicular to plane).
+
+    Examples
+    --------
+    >>> from os.path import join
+    >>> structure = load_structure(join(path_to_structures, "3wip.cif"), include_bonds=True, extra_fields=["charge"])
+    >>> interactions = find_pi_cation_interactions(structure)
+    >>> for ring_indices, cation_index in interactions:
+    ...     print(
+    ...         structure.res_name[ring_indices[0]],
+    ...         structure.res_name[cation_index]
+    ...     )
+    TYR ACH
+    TRP ACH
+    """
+    if atoms.bonds is None:
+        raise BadStructureError("Structure must have an associated BondList")
+
+    if atoms.charge is None:
+        raise BadStructureError(
+            "Structure must have a 'charge' annotation to identify cations."
+        )
+
+    rings = find_aromatic_rings(atoms)
+    if len(rings) == 0:
+        return []
+
+    cation_mask = atoms.charge > 0
+    cation_indices = np.where(cation_mask)[0]
+
+    if len(cation_indices) == 0:
+        return []
+
+    # Calculate ring centroids and normals
+    ring_centroids = np.array(
+        [atoms.coord[atom_indices].mean(axis=0) for atom_indices in rings]
+    )
+    ring_normals = np.array(
+        [_get_ring_normal(atoms.coord[atom_indices]) for atom_indices in rings]
+    )
+
+    cation_coords = atoms.coord[cation_indices]
+
+    # Create an index array that contains the Cartesian product of all rings and cations
+    indices = np.stack(
+        [
+            np.repeat(np.arange(len(rings)), len(cation_indices)),
+            np.tile(np.arange(len(cation_indices)), len(rings)),
+        ],
+        axis=-1,
+    )
+
+    ## Condition 1: Ring centroids and cations are close enough to each other
+    diff = displacement(ring_centroids[indices[:, 0]], cation_coords[indices[:, 1]])
+    # Use squared distance to avoid time consuming sqrt computation
+    sq_distance = vector_dot(diff, diff)
+    is_interacting = sq_distance < distance_cutoff**2
+    indices = indices[is_interacting]
+
+    ## Condition 2: Angle between ring normal and centroid-cation vector
+    diff = displacement(ring_centroids[indices[:, 0]], cation_coords[indices[:, 1]])
+    norm_vector(diff)
+    angles = _minimum_angle(ring_normals[indices[:, 0]], diff)
+    is_interacting = _is_within_tolerance(angles, 0, angle_tol)
+    indices = indices[is_interacting]
+
+    # Only return pairs where all conditions were fulfilled
+    return [(rings[ring_i], cation_indices[cation_j]) for ring_i, cation_j in indices]
+
+
 def _get_ring_normal(ring_coord):
     """
     Get the normal vector perpendicular to the ring plane.

biotite/version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.3.0'
-__version_tuple__ = version_tuple = (1, 3, 0)
+__version__ = version = '1.4.0'
+__version_tuple__ = version_tuple = (1, 4, 0)

{biotite-1.3.0.dist-info → biotite-1.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biotite
-Version: 1.3.0
+Version: 1.4.0
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite

{biotite-1.3.0.dist-info → biotite-1.4.0.dist-info}/RECORD

@@ -2,7 +2,7 @@ biotite/__init__.py,sha256=gzqOy5P7Zf667uYuUwqjLLW0GiBdqc23NLcZaXMuHKw,563
 biotite/copyable.py,sha256=Qnja44k58dAc3WkIUM0svqrbvqO9pSV-Atr9MUJSoCI,1968
 biotite/file.py,sha256=ktpRUk0OH5_wKIJHtCX3zDjXeJ3eQ4ycDjpp7HttUYM,6977
 biotite/setup_ccd.py,sha256=9StRz4qPVdTJNrPUoA_liwvkKnTb8O0U8PDxt1tDVwc,6248
-biotite/version.py,sha256=gjq5-5A1fJztrO0JABjZYm7eEvg0FysPGOYPEkyBwM8,532
+biotite/version.py,sha256=mQpvfIn8roT-O8LS07P1pK-7O17jWuq_vL-TTh8VVvs,532
 biotite/visualize.py,sha256=z4lBfJAt5YxGqtgxgcLHKMwVcE4u6fqExEyrOHcSiaY,14330
 biotite/application/__init__.py,sha256=Rei3EwlpCnC_cJNQoTJYY_Gw_qLdsqgnRxV5b1slHJU,3148
 biotite/application/application.py,sha256=J9ydVvN_5C3nYuLl12EPBhM67i0GQm6MPy0F1K-jdgc,8372
@@ -65,11 +65,11 @@ biotite/interface/pymol/__init__.py,sha256=fL56vVJ0Ro-3aftoE3lBVRmwPRl2iHWhsnSEB
 biotite/interface/pymol/cgo.py,sha256=naAQ-5R2wpsbXy3UkjkFvGkzRx8xVr53qlGpltyRO8I,10205
 biotite/interface/pymol/convert.py,sha256=mukBkBjGO0kv5Ec_ALG9i3BPYUCap1Zf1LiIJvBLrZw,6229
 biotite/interface/pymol/display.py,sha256=R8vgVRoByPr_mkhm81fJdtzyZCMzRj8jyfviNPAfTLU,8725
-biotite/interface/pymol/object.py,sha256=t_sT7lu1Vh_jC0uzzv7ydSf02jzeClT4tfiPN9fIMyY,45419
+biotite/interface/pymol/object.py,sha256=-eegu5qwye8_WE_89baCsk7nfqeHpQo50VoXPa4dCjA,45508
 biotite/interface/pymol/shapes.py,sha256=w0_fBczmPtI3tQrmrwOp8owg6WUfhX3qXhKXibtfwBA,6244
 biotite/interface/pymol/startup.py,sha256=vHdpd3RusQXJr9PSPbJxWbo8CuJSN4YpecNCM0az1Ak,4788
 biotite/interface/rdkit/__init__.py,sha256=0hPcE6j-HKorkcFq3thhx6k2BEjeo0bbwuCGTEqB5YI,551
-biotite/interface/rdkit/mol.py,sha256=GH0iSrs54qNWSZbVjPw3T0hjJbTWkCFjTwpq8ef7XTI,20134
+biotite/interface/rdkit/mol.py,sha256=EbNDkS0EqjJ6IxDIJHrAjMParbIDkfZpjjRY9R9L5M8,20119
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